The view is toward the interface between the 30S and 50S subunits. 16S rRNA is colored blue. The proteins are colored by Chain ("rainbow colors"). The published coordinates, 1gix.pdb, specify the atomic postitions for the tRNAs and the mRNA; otherwise, only the alpha carbons of proteins or phosphorous atoms of rRNA are known. Therefore, Backbone (thick and thin) or Spacefill are the only displays possible.
The numbered "Highlight" buttons above display details of the 30S structure. The following paragraphs briefly describe the displays.
1. RNA and Protein Features.
a. The 16S rRNA domains are thick backbone, colored as follows: blue, 5' domain, or "Body"; magenta, central domain, or "Platform"; red, 3' major domain, or "Head"; and yellow, 3' minor domain, or "Neck". Proteins are red.
b. The tRNAs are thick backbone; the A, P, and E sites are colored green, magenta, and orange, respectively. mRNA (U6) is Spacefill, colored CPK. The anticodons and 3' terminal adenosines (residue 76) are Spacefill, colored CPK; the P-site tRNA is labelled "peptide" at its 3' OH.
c. The protein subunits are colored Group and labelled at their N-termini.
2. Interactions
a. The Intersubunit Bridges are primarily RNA-RNA interactions.
S13 and S15 are the only small subunit proteins that interact with the
50S subunit. The individual residues are Spacefill, colored white. See
Yusupov, et al. Table 2 for details.
b. The tRNA-30S Subunit Contacts are also largely RNA-RNA;
S7, S9, S12, and S13 are the only proteins involved. For the following
three buttons, the 30S residues making contacts are Spacefill; RNA is white;
protein is yellow. The tRNA residues making these contacts are Sticks,
colored cyan. See Yusupov, et al. Table 3 for details.
The P-Site tRNA contacts Arg 128 of S9 and several
S13 residues. The other contacts are to 16S rRNA or to mRNA.
The A-Site tRNA contacts S12 and additional residues
on S13.
The E-Site tRNA contacts relatively large portions
of a b-hairpin and an a-helix
of S7.
Viewing Tip: After highlighting the protein residues above,
select the chain and color it yellow to see the unusual serpentine shapes
of many of them. For example, the sequence of Chime menu steps might be:
Select¬Chain¬P; then Select¬Change Color To¬Yellow.
c. The Codon-Anticodon close-up is shown as Sticks-Ball
& Stick, colored CPK, with the tRNA backbones colored green or magenta.
The tRNA anticodons and the six residues of mRNA are labelled at their
5' phosphates. Each codon-anticodon base pairing interaction corresponds
to a standard A-form RNA (mini) helix; however, a kink at the U4 phosphate
of mRNA prevents the structure from being a continuous double helix.
The 25 protein and RNA chains in the 30S model are coded with uppercase letters. The complete listing of chains and standard subunit names is on a separate (pop-up) page, 30S Ribosome Chain and Subunit Terminology.
Page Top
The 30S subunit structure is described in Yusupov, M.
M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J.
H. D., Noller, H. F. (2001) "Crystal structure of the ribosome at 5.5 Å
resolution" Science 292:883. PubMed.
